On-Prem Cluster Computing

Jon Willcox (willcox@broadinstitute.org)

03/26/2024

These are some instructions to get set up for on-prem cluster computing in the Ellinor Lab at The Broad Institute.

Step 1: Getting access to /medpop/afib

Submit request here

Patrick will have to give the ok, but that’s usually quick.

Once you have access, you can log on with the command below if you are on-site or connected to the Broad VPN.

# Replace 'userid' with your user ID
ssh userid@login.broadinstitute.org

Step 2: Set up authentication key pair

This will let you login to the cluster from your laptop without using a password.

BITS instructions are here

Step 3: Set up to transfer files

If you have a Broad-issued computer, you can map a network drive to your computer

BITS instructions are here

Ellinor Lab servers:

directory	server
/medpop/afib	smb://helium/medpop_afib
/medpop/bayercvd	smb://hydrogen/medpop_bayercvd

For non-Broad-issued computers BITS instructions are here

Step 4 (optional): Customize bash configuration

The following lines set a few defaults that may be useful:

# Include a path with some useful scripts 
PATH=$PATH:/medpop/afib/willcox/bin

# automatically load UGER on openening session
use UGER

# Reset LESS default
LESS=-c

        # the following lines should go within the if-statment,
        #   e.g. just before the line 'fi'

        # load a few commonly used dotkits
        use .google-cloud-sdk
        use .anaconda3-2022.10
        use GCC-5.2
        use R-4.1

These can be added to the file ~/.my.bashrc using an editor such as vim or nano, or if you'd prefer, you can copy a template using the following lines:

# save your current ~/.my.bashrc as ~/.my.bashrc.backup
mv ~/.my.bashrc ~/.my.bashrc.backup

# copy the template over to ~/.my.bashrc
cp /medpop/afib/willcox/resources/.my.bashrc ~/.my.bashrc

Step 5: Make yourself a working directory

For example, if you will mainly be working in /medpop/afib, you can use the command:

# Replace userid with your user ID
mkdir /medpop/afib/userid

This will be a location for you to store data and perform operations.

Useful resources and commands

• Here is a useful tutorial to learn basics for operating in a linux/command-line environment.
• Here is a useful tutorial for learning the basics of Bash.

Because space on-prem is limited, it is helpful to keep tabs on your disk usage:

# This command will display some basic information about availible space on your filesystem
# Replace '/medpop/afib' with the filesystem you would like to check
df -h /medpop/afib

# This command will display the disk usage for your working directory
# Replace userid with your user ID
du -sh /medpop/afib/userid